Journal of Biomolecular Structure and Dynamics, Volume 42, Issue 10 (2024)

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Journal of Biomolecular Structure and Dynamics, Volume 42, Issue 10 (2024)

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Research Articles

Article
T cell epitope based vaccine design while targeting outer capsid proteins of rotavirus strains infecting neonates: an immunoinformatics approach
Arijit Das Sharma, Ravneet Kaur Grewal, Suresh Gorle, Andrés Felipe Cuspoca, Vikas Kaushik, Abdul Rajjak Shaikh, Luigi Cavallo & Mohit Chawla
Pages: 4937-4955
Published online: 29 Jun 2023
AbstractforT cell epitope based vaccine design while targeting outer capsid proteins of rotavirus strains infecting neonates: an immunoinformatics approach | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
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Article
Base pairs with 5-chloroorotic acid and comparison with the natural nucleobase. Structural and spectroscopic study, and three suggested antiviral modified nucleosides
M. Alcolea Palafox, D. Kattan, M. L. de Pedraza Velasco, J. Isasi, Kaushal Rani, S. P. Singh, J. K. Vats & V. K. Rastogi
Pages: 4956-4984
Published online: 04 Jul 2023
AbstractforBase pairs with 5-chloroorotic acid and comparison with the natural nucleobase. Structural and spectroscopic study, and three suggested antiviral modified nucleosides | Full Text | References | PDF (3.7 MB) | EPUB | Supplemental
  • 45 Views
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Article
Explore the underlying oral efficacy of α-, β-, γ-Cyclodextrin against the ulcerative colitis using in vitro and in vivo studies assisted by network pharmacology
Weiqin Wang, Xuefeng Li, Hangyi Wu, Fanli Shi, Zhenhai Zhang & Huixia Lv
Pages: 4985-5000
Published online: 30 Jul 2023
AbstractforExplore the underlying oral efficacy of α-, β-, γ-Cyclodextrin against the ulcerative colitis using in vitro and in vivo studies assisted by network pharmacology | Full Text | References | PDF (3 MB) | EPUB | Supplemental
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Article
In silico identification of cyclosporin derivatives as potential inhibitors for RdRp of rotavirus by molecular docking and molecular dynamic studies
Prashasti Sinha & Anil Kumar Yadav
Pages: 5001-5014
Published online: 30 Jul 2023
AbstractforIn silico identification of cyclosporin derivatives as potential inhibitors for RdRp of rotavirus by molecular docking and molecular dynamic studies | Full Text | References | PDF (2.5 MB) | EPUB
  • 100 Views
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Article
Anti-aging activity of Syn-Ake peptide by in silico approaches and in vitro tests
Bahar Gok, Yasemin Budama-Kilinc & Serda Kecel-Gunduz
Pages: 5015-5029
Published online: 22 Jun 2023
AbstractforAnti-aging activity of Syn-Ake peptide by in silico approaches and in vitro tests | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 287 Views
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Article
Glycosylation and charge distribution orchestrates the conformational ensembles of a biotechnologically promissory phytase in different pHs – a computational study
Thaís P. P. De Souza, Letícia Xavier Silva Cantão, Marina Quádrio Raposo Branco Rodrigues, Daniel Bonoto Gonçalves, Ronaldo Alves Pinto Nagem, Rafael Eduardo Oliveira Rocha, Renato Ramos Godoi, William James Nogueira Lima, Alexsandro Sobreira Galdino, Raquel Cardoso de Melo Minardi & Leonardo Henrique França de Lima
Pages: 5030-5041
Published online: 16 Jun 2023
AbstractforGlycosylation and charge distribution orchestrates the conformational ensembles of a biotechnologically promissory phytase in different pHs – a computational study | Full Text | References | PDF (2 MB) | EPUB | Supplemental
  • 140 Views
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Article
Conformational perturbation of SARS-CoV-2 spike protein using N-acetyl cysteine: an exploration of probable mechanism of action to combat COVID-19
Utsab Debnath, Amrita Mitra, Varun Dewaker, Yenamandra S. Prabhakar, Raghu Tadala, Kiran Krishnan, Padmakar Wagh, Umashankar Velusamy, Aastha Baliyan, Anura V. Kurpad, Parthasarathi Bhattacharyya & Amit Kumar Mandal
Pages: 5042-5052
Published online: 21 Jul 2023
AbstractforConformational perturbation of SARS-CoV-2 spike protein using N-acetyl cysteine: an exploration of probable mechanism of action to combat COVID-19 | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 98 Views
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Article
New tetrahydroisoquinoline-4-carbonitrile derivatives as potent agents against cyclin-dependent kinases, crystal structures, and computational studies
Youness El Bakri, Subramani Karthikeyan, Chin-Hung Lai, Etify A. Bakhite, Iqrar Ahmad, Abdu E. Abdel-Rahman, Suzan Abuelhassan, Islam S. Marae, Shaaban K. Mohamed & Joel T. Mague
Pages: 5053-5071
Published online: 26 Jun 2023
AbstractforNew tetrahydroisoquinoline-4-carbonitrile derivatives as potent agents against cyclin-dependent kinases, crystal structures, and computational studies | Full Text | References | PDF (3.5 MB) | EPUB | Supplemental
  • 95 Views
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Article
Computational screening of pathogenic missense nsSNPs in heme oxygenase 1 (HMOX1) gene and their structural and functional consequences
Arvind Kumar Yadav, T. P. Krishna Murthy, Gangaraju Divyashri, Durga Prasad N.Sriraksha Prakash, Vijaya Vaishnavi V.Rohit Shukla & Tiratha Raj Singh
Pages: 5072-5091
Published online: 11 Jul 2023
AbstractforComputational screening of pathogenic missense nsSNPs in heme oxygenase 1 (HMOX1) gene and their structural and functional consequences | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 139 Views
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Article
Structural and functional insights into a novel homozygous missense pathogenic variant in CUL7 identified in consanguineous Pakistani family
Ayesha Zaka, Maha Yousaf, Shaheen Shahzad, Hadi Zahid Rao, Jia Nee Foo & Saima Siddiqi
Pages: 5092-5103
Published online: 22 Jun 2023
AbstractforStructural and functional insights into a novel homozygous missense pathogenic variant in CUL7 identified in consanguineous Pakistani family | Full Text | References | PDF (3.3 MB) | EPUB | Supplemental
  • 167 Views
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Article
Levoleucovorin inhibits LOXL2 (lysyl oxidase like-2) to control breast cancer proliferation: a repurposing approach
Hemali Deshpande
Pages: 5104-5113
Published online: 20 Jun 2023
AbstractforLevoleucovorin inhibits LOXL2 (lysyl oxidase like-2) to control breast cancer proliferation: a repurposing approach | Full Text | References | PDF (1.7 MB) | EPUB
  • 150 Views
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Article
Hsa_circRNA_0000284 acts as a ceRNA to participate in coronary heart disease progression by sponging miRNA-338-3p via regulating the expression of ETS1
PhongSon Dinh, ChauMyThanh Tran, ThiPhuongHoai Dinh, Awais Ali & ShangLing Pan
Pages: 5114-5127
Published online: 19 Jun 2023
AbstractforHsa_circRNA_0000284 acts as a ceRNA to participate in coronary heart disease progression by sponging miRNA-338-3p via regulating the expression of ETS1 | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 231 Views
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Article
Mechanism of Xiaoyao San in treating non-alcoholic fatty liver disease with liver depression and spleen deficiency: based on bioinformatics, metabolomics and in vivo experiments
Xiaofeng Ruan, Xiaoming Zhang, Liming Liu & Jianjun Zhang
Pages: 5128-5146
Published online: 13 Jul 2023
AbstractforMechanism of Xiaoyao San in treating non-alcoholic fatty liver disease with liver depression and spleen deficiency: based on bioinformatics, metabolomics and in vivo experiments | Full Text | References | PDF (9.2 MB) | EPUB | Supplemental
  • 229 Views
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Article
Interaction studies of cannabidiol with human serum albumin by surface plasmon resonance, spectroscopy, and molecular docking
Himanshu Paliwal, Sunisa Kaewpaiboon, Muhammad Ali Khumaini Mudhar Bintang & Teerapol Srichana
Pages: 5147-5158
Published online: 11 Jul 2023
AbstractforInteraction studies of cannabidiol with human serum albumin by surface plasmon resonance, spectroscopy, and molecular docking | Full Text | References | PDF (2.2 MB) | EPUB
  • 161 Views
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Article
Evaluation of Cordyceps militaris steroids as anti-inflammatory agents to combat the Covid-19 cytokine storm: a bioinformatics and structure-based drug designing approach
Manmeet Singh, Himanshu Verma, Narendra Gera, Raju Baddipadige, Shalki Choudhary, Priyanka Bhandu & Om Silakari
Pages: 5159-5177
Published online: 07 Aug 2023
AbstractforEvaluation of Cordyceps militaris steroids as anti-inflammatory agents to combat the Covid-19 cytokine storm: a bioinformatics and structure-based drug designing approach | Full Text | References | PDF (4.2 MB) | EPUB
  • 123 Views
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Article
Identification of potential biogenic chalcones against antibiotic resistant efflux pump (AcrB) via computational study
Sanket Rathod, Sreenath Dey, Swaranjali Pawar, Rakesh Dhavale, Prafulla Choudhari, Eerappa Rajakumara, Deepak Mahuli, Durgacharan Bhagwat, Yasinalli Tamboli, Poournima Sankpal, Sachin Mali & Harinath More
Pages: 5178-5196
Published online: 20 Jun 2023
AbstractforIdentification of potential biogenic chalcones against antibiotic resistant efflux pump (AcrB) via computational study | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 123 Views
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Article
Repurposing phytochemicals of Citrullus colocynthis against maltase-glucoamylase using molecular docking, MMGBSA, MD simulation and linear regression to identify potential anti-diabetic compounds
Parameswar Sahu, Rosaleen Sahoo, Abhishek Kumar Sahu, Sundeep Singh Saluja & Banshidhar Behera
Pages: 5197-5206
Published online: 22 Jun 2023
AbstractforRepurposing phytochemicals of Citrullus colocynthis against maltase-glucoamylase using molecular docking, MMGBSA, MD simulation and linear regression to identify potential anti-diabetic compounds | Full Text | References | PDF (1.4 MB) | EPUB | Supplemental
  • 113 Views
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Article
Interaction of systemic drugs causing ocular toxicity with organic cation transporter: an artificial intelligence prediction
Manisha Malani, Manthan S. Hiremath, Surbhi Sharma, Manisha Jhunjhunwala, Shovanlal Gayen, Chittaranjan Hota & Jayabalan Nirmal
Pages: 5207-5218
Published online: 20 Jun 2023
AbstractforInteraction of systemic drugs causing ocular toxicity with organic cation transporter: an artificial intelligence prediction | Full Text | References | PDF (1.7 MB) | EPUB | Supplemental
  • 159 Views
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Article
A multitier virtual screening study of phytoconstituents as Myeloid Cell Leukemias 1 inhibitors
Wenjun Liu, Mohammad Khalid, Shadma Wahab, Mohd Faizan Siddiqui, Shaheer Hasan Khan, Mohd Sadiq & Zeenat Khatoon
Pages: 5219-5228
Published online: 07 Jul 2023
AbstractforA multitier virtual screening study of phytoconstituents as Myeloid Cell Leukemias 1 inhibitors | Full Text | References | PDF (1.2 MB) | EPUB | Supplemental
  • 132 Views
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Article
In silico-based screening of natural products as potential inhibitors of SARS-CoV-2 macrodomain 1
Song Xie, Shoujing Cao, Juhong Wu, Zhinuo Xie, Yu-Tsen Liu, Wei Fu, Qianqian Zhao, Lin Liu, Lin Yang & Jinyu Li
Pages: 5229-5237
Published online: 22 Jun 2023
AbstractforIn silico-based screening of natural products as potential inhibitors of SARS-CoV-2 macrodomain 1 | Full Text | References | PDF (1.5 MB) | EPUB | Supplemental
  • 90 Views
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Article
Temperature effect in the inhibition of PLA2 activity of Bothrops brazili venom by Rosmarinic and Chlorogenic acids, experimental and computational approaches
Eduardo Augusto da Silva Diniz, Diana Pontes da Silva, Sarah de Sousa Ferreira, Matheus de Freitas Fernandes-Pedrosa & Davi Serradella Vieira
Pages: 5238-5252
Published online: 28 Jun 2023
AbstractforTemperature effect in the inhibition of PLA2 activity of Bothrops brazili venom by Rosmarinic and Chlorogenic acids, experimental and computational approaches | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 115 Views
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Article
Virtual screening and molecular growth guide the design of inhibitors for the influenza virus drug-resistant mutant M2-V27A/S31N
Changyong Deng, Xiaobo Wang, Tangle Wang, Wei Liu, Xiaolan Yuan, Yan Huang & Shuang Cao
Pages: 5253-5267
Published online: 09 Jul 2023
AbstractforVirtual screening and molecular growth guide the design of inhibitors for the influenza virus drug-resistant mutant M2-V27A/S31N | Full Text | References | PDF (2.2 MB) | EPUB
  • 120 Views
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Article
Computational investigation of imidazo[2,1-b]oxazole derivatives as potential mutant BRAF kinase inhibitors: 3D-QSAR, molecular docking, molecular dynamics simulation, and ADMETox studies
Meryem Boutalaka, Salma El bahi, Marwa Alaqarbeh, Moulay Ahfid El Alaouy, Yassine Koubi, Khalil El Khatabi, Hamid Maghat, Mohammed Bouachrine & Tahar Lakhlifi
Pages: 5268-5287
Published online: 09 Jul 2023
AbstractforComputational investigation of imidazo[2,1-b]oxazole derivatives as potential mutant BRAF kinase inhibitors: 3D-QSAR, molecular docking, molecular dynamics simulation, and ADMETox studies | Full Text | References | PDF (2.9 MB) | EPUB
  • 134 Views
  • 6 CrossRef citations
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Article
An immuno-informatics approach for annotation of hypothetical proteins and multi-epitope vaccine designed against the Mpox virus
Md. Hridoy Ahmed, Nure Sharaf Nower Samia, Gagandeep Singh, Vandana Gupta, Mohammed Faizan Mohammed Mishal, Alomgir Hossain, Kamrul Hassan Suman, Adnan Raza, Amit Kumar Dutta, Moriom Akhter Labony, Jakia Sultana, Emdadul Haque Faysal, Sulaiman Mohammed Alnasser, Prawez Alam & Faizul Azam
Pages: 5288-5307
Published online: 31 Jul 2023
AbstractforAn immuno-informatics approach for annotation of hypothetical proteins and multi-epitope vaccine designed against the Mpox virus | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 567 Views
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Article
Pharmacophore-based virtual screening, molecular docking and molecular dynamics studies for the discovery of novel neuraminidase inhibitors
Bourougaa Lotfi, Ouassaf Mebarka, Shafi Ullah Khan & Thet Thet Htar
Pages: 5308-5320
Published online: 19 Jun 2023
AbstractforPharmacophore-based virtual screening, molecular docking and molecular dynamics studies for the discovery of novel neuraminidase inhibitors | Full Text | References | PDF (1.8 MB) | EPUB
  • 163 Views
  • 3 CrossRef citations
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Article
Field-based 3D-QSAR for tyrosine protein kinase JAK-2 inhibitors
Sowmya Andole, Gouthami Thumma, Rajasekhar Reddy Alavala & Kiran Gangarapu
Pages: 5321-5333
Published online: 06 Jul 2023
AbstractforField-based 3D-QSAR for tyrosine protein kinase JAK-2 inhibitors | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
  • 151 Views
  • 1 CrossRef citations
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Article
Copper transporter protein (MctB) as a therapeutic target to elicit antimycobacterial activity against tuberculosis
Manish Dwivedi, Sandra Jose, Megha Gupta, Sreevidya S. Devi, Ritu Raj & Dinesh Kumar
Pages: 5334-5348
Published online: 20 Jun 2023
AbstractforCopper transporter protein (MctB) as a therapeutic target to elicit antimycobacterial activity against tuberculosis | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 142 Views
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Article
Identification of novel T-cell epitopes on monkeypox virus and development of multi-epitopes vaccine using immunoinformatics approaches
Wahiba Ezzemani, Ahd Ouladlahsen, Haya Altawalah, Rachid Saile, M’hammed Sarih, Anass Kettani & Sayeh Ezzikouri
Pages: 5349-5364
Published online: 24 Jun 2023
AbstractforIdentification of novel T-cell epitopes on monkeypox virus and development of multi-epitopes vaccine using immunoinformatics approaches | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 151 Views
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Article
Differential glycosylation in mutant vitamin D-binding protein decimates the binding stability of vitamin D
Usama, Zahid Khan, Aktar Ali, Masaud Shah & Muhammad Imran
Pages: 5365-5375
Published online: 25 Jun 2023
AbstractforDifferential glycosylation in mutant vitamin D-binding protein decimates the binding stability of vitamin D | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 127 Views
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Article
Design, synthesis, computational molecular docking studies of novel heterocyclics bearing 1,2,4–triazole, 1,3,4–oxadiazole conjugates as potent antibacterial and antitubercular agents
B. Sravanthi, G. Himavathi, A. R. Robert, Prashantha Karunakar, K. S. Kiran & S. Maddila
Pages: 5376-5389
Published online: 20 Jun 2023
AbstractforDesign, synthesis, computational molecular docking studies of novel heterocyclics bearing 1,2,4–triazole, 1,3,4–oxadiazole conjugates as potent antibacterial and antitubercular agents | Full Text | References | PDF (2.6 MB) | EPUB | Supplemental
  • 218 Views
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Article
Probing some recent natural compounds from Phellinus baumii, Colletotrichum sp. and Ligustrum lucidum as heat shock protein 90 inhibitors
Taner Erdogan & Fatma Oguz Erdogan
Pages: 5390-5401
Published online: 20 Jun 2023
AbstractforProbing some recent natural compounds from Phellinus baumii, Colletotrichum sp. and Ligustrum lucidum as heat shock protein 90 inhibitors | Full Text | References | PDF (3.4 MB) | EPUB | Supplemental
  • 91 Views
  • 2 CrossRef citations
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Article
Allosteric inhibition of dengue virus RNA-dependent RNA polymerase by Litsea cubeba phytochemicals: a computational study
Hrithika Panday, Saurabh Kumar Jha, Mohammed Al-Shehri, Siva Prasad Panda, Rashmi Rana, Nada F. Alwathinani, Esam I. Azhar, Vivek Dhar Dwivedi & Abhimanyu Kumar Jha
Pages: 5402-5414
Published online: 26 Jun 2023
AbstractforAllosteric inhibition of dengue virus RNA-dependent RNA polymerase by Litsea cubeba phytochemicals: a computational study | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 150 Views
  • 2 CrossRef citations
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Article
Dalbergia sissoo phytochemicals as EGFR inhibitors: an in vitro and in silico approach
Hem N. Naik, Dilip Kanjariya, Shahnaz Parveen, Abha Meena, Iqrar Ahmad, Harun Patel, Ramavatar Meena & Smita Jauhari
Pages: 5415-5427
Published online: 02 Jul 2023
AbstractforDalbergia sissoo phytochemicals as EGFR inhibitors: an in vitro and in silico approach | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 182 Views
  • 4 CrossRef citations
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Article
Development, validation and analysis of a human profurin 3D model using comparative modeling and molecular dynamics simulations
Brenda de Souza Ferrari, Camilo Henrique da Silva Lima & Magaly Girão Albuquerque
Pages: 5428-5446
Published online: 14 Jul 2023
AbstractforDevelopment, validation and analysis of a human profurin 3D model using comparative modeling and molecular dynamics simulations | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 137 Views
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Article
Computational and experimental examinations of new antitumor palladium(II) complex: CT-DNA-/BSA-binding, in-silico prediction, DFT perspective, docking, molecular dynamics simulation and ONIOM
Ashraf Sadat Dorafshan Tabatabai, Effat Dehghanian, Hassan Mansouri-Torshizi & Mehran Feizi-Dehnayebi
Pages: 5447-5469
Published online: 22 Jun 2023
AbstractforComputational and experimental examinations of new antitumor palladium(II) complex: CT-DNA-/BSA-binding, in-silico prediction, DFT perspective, docking, molecular dynamics simulation and ONIOM | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 175 Views
  • 18 CrossRef citations
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Rapid Communication

Rapid Communication
Self-inhibition of HER2 and HER3 at fever temperatures may prevent their hetero-dimerization
Puneet Kumar Singh & Razvan C. Stan
Pages: 5470-5473
Published online: 21 Jun 2023
AbstractforSelf-inhibition of HER2 and HER3 at fever temperatures may prevent their hetero-dimerization | Full Text | References | PDF (703.2 KB) | EPUB | Supplemental
  • 48 Views
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